RetrogeneDB ID: retro_opri_1016

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5809:21422..21746(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: UBA52
• Ensembl ID: ENSOPRG00000004784
• Aliases: None
• Description: ubiquitin A-52 residue ribosomal protein fusion product 1 [Source:HGNC Symbol;Acc:12458]

Sequence

>retro_opri_1016
GTAGATCCTTGTGAAGACTCTGAAAATGTCAAGGCGAAGACCCAGAACAAAGAGGGCATCCTCCCGGACCAGCAGCATCT
TATCTTTGCCGGCAAGCCTCTGGAGGACGGTGGCACTCTGTGGGACTACAACATCCAGGAAGAGTGCACACTGCACCTGG
TGCTCCACCTGCAGGGCGGCATCATTGAGCAGTCCCTGCGCCAGCTCGCCCAGAAGTTACCACTGTGACAATATGATCTG
CTGCAAGTGCAACGCCCACCTGCACCCCTGCGCCCTCAACTGCCGCTGAGAAAACGCCGCCACACCAACAGCCTGCGCCC
CAAG

Alignment

ORF - retro_opri_1016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.82 %
• Parental protein coverage: 84.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGIIEPSLRQLA
          V.P....ENVKAK.Q.KEGI.PDQQ.LIFAGK.LEDG.TL.DYNIQ.E.TLHLVL.L.GGIIE.SLRQLA
Retrocopy VDPCEDSENVKAKTQNKEGILPDQQHLIFAGKPLEDGGTLWDYNIQEECTLHLVLHLQGGIIEQSLRQLA

Parental  QK-YNCDKMICRKCYARLHPRAVNCR-KKKCGHTNNLRPK
          QK.Y.CD.MIC.KC.A.LHP.A.NCR...K..HTN.LRPK
Retrocopy QK>YHCDNMICCKCNAHLHPCALNCR<LRKRRHTNSLRPK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_1016 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011356	10 retrocopies	retro_amel_1045, retro_amel_1416, retro_amel_1455, retro_amel_1759, retro_amel_1849, retro_amel_214, retro_amel_800, retro_amel_904, retro_amel_941, retro_amel_973,
Bos taurus	ENSBTAG00000007737	3 retrocopies	retro_btau_1059, retro_btau_1318, retro_btau_832,
Callithrix jacchus	ENSCJAG00000007470	22 retrocopies	retro_cjac_1363, retro_cjac_1388, retro_cjac_1426, retro_cjac_1485, retro_cjac_1521, retro_cjac_1561, retro_cjac_1731, retro_cjac_1743, retro_cjac_2002, retro_cjac_207, retro_cjac_2254, retro_cjac_2292, retro_cjac_2413, retro_cjac_2501, retro_cjac_2505, retro_cjac_2898, retro_cjac_3054, retro_cjac_658, retro_cjac_683, retro_cjac_883, retro_cjac_892, retro_cjac_898,
Equus caballus	ENSECAG00000020660	8 retrocopies	retro_ecab_1014, retro_ecab_107, retro_ecab_313, retro_ecab_641, retro_ecab_772, retro_ecab_835, retro_ecab_836, retro_ecab_857,
Felis catus	ENSFCAG00000009745	14 retrocopies	retro_fcat_1159, retro_fcat_1204, retro_fcat_1226, retro_fcat_1232, retro_fcat_1382, retro_fcat_1428, retro_fcat_1449, retro_fcat_1540, retro_fcat_1661, retro_fcat_86, retro_fcat_876, retro_fcat_909, retro_fcat_939, retro_fcat_989,
Homo sapiens	ENSG00000221983	2 retrocopies	retro_hsap_2622, retro_hsap_4004,
Latimeria chalumnae	ENSLACG00000008132	1 retrocopy	retro_lcha_11,
Mustela putorius furo	ENSMPUG00000015527	8 retrocopies	retro_mputfur_1059, retro_mputfur_1119, retro_mputfur_1126, retro_mputfur_382, retro_mputfur_516, retro_mputfur_713, retro_mputfur_78, retro_mputfur_945,
Mus musculus	ENSMUSG00000090137	3 retrocopies	retro_mmus_101, retro_mmus_129, retro_mmus_31,
Ochotona princeps	ENSOPRG00000004784	6 retrocopies	retro_opri_1016 , retro_opri_144, retro_opri_219, retro_opri_458, retro_opri_644, retro_opri_787,
Pongo abelii	ENSPPYG00000009746	2 retrocopies	retro_pabe_111, retro_pabe_3291,
Pan troglodytes	ENSPTRG00000039223	8 retrocopies	retro_ptro_1142, retro_ptro_1767, retro_ptro_2607, retro_ptro_2718, retro_ptro_2815, retro_ptro_792, retro_ptro_895, retro_ptro_919,
Rattus norvegicus	ENSRNOG00000019974	7 retrocopies	retro_rnor_1125, retro_rnor_1458, retro_rnor_2115, retro_rnor_2472, retro_rnor_2487, retro_rnor_2901, retro_rnor_944,
Sarcophilus harrisii	ENSSHAG00000007075	3 retrocopies	retro_shar_405, retro_shar_434, retro_shar_703,
Ictidomys tridecemlineatus	ENSSTOG00000004678	1 retrocopy	retro_itri_49,
Xiphophorus maculatus	ENSXMAG00000003911	1 retrocopy	retro_xmac_6,